The genes for trophoblast interferons (IFN) bovine trophoblast protein-1 (bTP-1) and ovine trophoblast protein-1 (oTP-1) are expressed massively in the trophectoderm of preimplantation bovine and ovine concepti during the period of maternal recognition of pregnancy. These 172-amino acid IFN are closely related to the IFN-alpha II, a family of "long" IFN expressed in virus-induced leukocytes. Genomic Southern blotting with a full-length bTP-1 cDNA revealed about 15 genes that bind the probe with varying intensities. By using more specific probes for the 3'-ends of the cDNA, we have shown that only four to five of these represent bTP-1 genes, whereas no more than another four are IFN-alpha II. Genes for bTP-1 and IFN-alpha II, all of which are intronless, have been isolated from bovine genomic libraries, and their nucleotide sequences were compared. Additional bTP-1 genes and two distinct oTP-1 genes have been isolated from bovine and ovine genomic DNA by using the polymerase chain reaction procedure in conjunction with specific 3'- and 5'- primers (derived from the bTP-1 gene sequences determined above). The promoter region up to 100 bases upstream from the transcription start sites of the trophoblast IFN are almost completely conserved across different genes and across species, yet show only limited sequence identity with IFN-alpha II. Two putative binding regions for interferon regulatory factor-1 as well as several GAAANN motifs (where N is any nucleotide) that have been implicated in viral responsiveness of alpha 1- and beta-IFN genes are retained at identical positions in all of the trophoblast genes. Putative interferon regulatory factor-1-binding nucleotide hexamers and GAAANN motifs are also present in the IFN-alpha II genes, but these are organized very differently than in the trophoblast IFN genes. A GAAATG motif is present in IFN-alpha II promoters but is absent in trophoblast IFN genes. Based on the evidence presented, it is proposed that the trophoblast interferons constitute a separate subclass of IFN-alpha distinct from IFN-alpha II and IFN-alpha I.